GlobalAncova

DOI: 10.18129/B9.bioc.GlobalAncova    

Global test for groups of variables via model comparisons

Bioconductor version: Release (3.8)

The association between a variable of interest (e.g. two groups) and the global pattern of a group of variables (e.g. a gene set) is tested via a global F-test. We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. The framework is generalized to groups of categorical variables or even mixed data by a likelihood ratio approach. Closed and hierarchical testing procedures are supported. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany and BMBF grant 01ZX1309B, Germany.

Author: U. Mansmann, R. Meister, M. Hummel, R. Scheufele, with contributions from S. Knueppel

Maintainer: Manuela Hummel <m.hummel at dkfz.de>

Citation (from within R, enter citation("GlobalAncova")):

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("GlobalAncova", version = "3.8")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("GlobalAncova")

 

PDF R Script GlobalAncova.pdf
PDF R Script GlobalAncovaDecomp.pdf
PDF   Reference Manual
Text   NEWS

Details

biocViews DifferentialExpression, Microarray, OneChannel, Pathways, Regression, Software
Version 4.0.0
In Bioconductor since BioC 1.7 (R-2.2) (13 years)
License GPL (>= 2)
Depends methods, corpcor, globaltest
Imports annotate, AnnotationDbi, Biobase, dendextend, GSEABase, VGAM
LinkingTo
Suggests GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
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Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package GlobalAncova_4.0.0.tar.gz
Windows Binary GlobalAncova_4.0.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) GlobalAncova_4.0.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/GlobalAncova
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/GlobalAncova
Package Short Url http://bioconductor.org/packages/GlobalAncova/
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